My perspective: I grew up in and around the military, I understand military command structures and I see them as distinct from our overall society. That doesn't mean that there is no place for that sort of structure within a society. Star Trek always appeared to me as representing that military structure within the overall structure of the Federation's society. In fact, most members of the Federation were not members of anything military-like (or so it's claimed in the show, you don't really see too much outside the ship and non-Federation planets). The ship, the Enterprise, never seemed like a metaphor for anything (the Federation, on the other hand, was clearly meant as an analog to the the US and most of Western Europe, or the direction Rodenberry thought they were headed).

> I've also seen it referred to as such by people wanting to create the perfect society.

I do not doubt that you've seen this. But I've, personally, only heard and read people reference the Federation as a perfect society, not the Enterprise. Until today.